The microbiological pollution of water is a serious environmental issue on an international scale. The pollution of water with human and animal waste is a source of hazardous pathogens and, unfortunately, contamination of natural water bodies poses a serious health risk. The microbiological quality of water (inland, coastal and transitional) is directed by the European Union (EU). Ireland must ensure at least good water quality by 2015. The aim of this study was to investigate pollution trends in rivers, canals and coastal waters under varying conditions, the cause of the contamination and to compare the findings with the limits as set out in the relevant EU directive. The results of this work showed that the poor quality of the rivers in Dublin city is strongly related to human activity. A case of a direct sewage contamination of the river Tolka is reported here. The water quality of the canals in the Dublin area was found to be excellent, however further evidence of the human influence on water quality was shown in the waters of the Grand Canal. The situation in the rural areas outside Dublin points to the fact that human sewage contributes to a lesser extend to the high levels of the microbial contamination in the River Tolka than when compared to the farming activities in the area. The extremely high faecal coliform counts that were registered in several water sources in the North County Dublin were thought to have a potential influence on the contamination of coastal waters at Balbriggan and Portrane.